Well to be fair on Nintendo, they do have to spread these games out over time. They can't simply say pick Resident Evil and release it, they have to ask Capcom about it. They can however release their own titles they've developed and publish but a lot were by Rare and some were licensed too.
Here is a list of games Nintendo published on the N64
*=already on VC
L=licensed game
R=Owned by Rare/Microsoft
1080° Snowboarding *
Banjo-Kazooie R
Banjo-Tooie R
Blast Corps R
Bomberman 64
Bomberman 64 2nd
Bomberman Hero
Command & Conquer
Conkers Bad Fur Day (in some places THQ published this)
Custom Robo (Japan only)
Custom Robo V2 (Japan only)
Cruis'N USA *
Diddy Kong Racing
Dōbutsu no Mori (Japan only)
Donkey Kong 64
Dr. Mario 64
Excitebike 64
F-Zero X *
GoldenEye 007 L
Hey You, Pikachu!
Itoi Shigesato's No. 1 Bass Fishing: Definitive Edition L (Japan only)
Jet Force Gemini R
Ken Griffey Jr.'s Slugfest L
Killer Instinct Gold R
Kirby 64 *
Kobe Bryant in NBA Courtside L
The Legend of Zelda: Majora's Mask *
The Legend of Zelda: Ocarina of Time
Major League Baseball Featuring Ken Griffey, Jr. L
Mario Golf *
Mario Kart 64 *
Mario Tennis
Mario Part 1-3
Mickey's Speedway USA L
Mischief Makers
NBA Courtside 2: Featuring Kobe Bryant L
The New Tetris
Paper Mario *
Perfect Dark R
PilotWings 64
Pokémon Puzzle League *
Pokemon Snap *
Pokémon Stadium
Pokémon Stadium 2
Ridge Racer 64
Sin and Punishment: Successor of the Earth * (Japan only)
Starfox 64 / Lylat Wars *
Star Wars: Episode I Racer L
Star Wars: Shadows of the Empire L
Starcraft 64
Super Mario 64 *
Super Smash Bros
Tetrisphere
Waialae Country Club: True Golf Classics
Wave Race 64 *
Yoshi's Story *
As you can see Nintendo have released quite a lot of what they can, but they also need to spread games out so that there are some more for the Wii & its successors lifespan. If they released twice as many games already then a couple of years down the line people will be moaning about the lack of N64 games coming out.
A lot of these games are licensed and some of these licenses belong to other companies, also these games will need Nintendo to get the license again, which costs them money. Most belong to Rare/Microsoft so they have to ask and yet again give them money for them.
You also have to take in to consideration that a lot of these games my be copyrighted to other people, these people may not allow Nintendo to release them for some reason. There are a lot of factors in this, Nintendo can't simply pick and choose from any game, not even the ones they have published themselves/
As for GoldenEye, it was Nintendo who were the ones holding it back. Microsoft were happy as long as they could do a version for the XBLA and they were also gonna let some of the profits of that go to Nintendo, but Nintendo were pissy and thought "nah nah fuck you, we only want it on VC". Activision who owns the bond name were also happy as long as they had a cut but again Nintendo wants to maximise profits with their games, I'm guessing that if they did release GoldenEye then some profit would have had to gone to Rare/Microsoft & some to Activision, and Nintendo see it as this; if people are buying GoldenEye on VC then they're not buying another game for which they may have had more profit from.